Variant report

Variant	rs9877722
Chromosome Location	chr3:135635468-135635469
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135634384..135636473-chr3:135692724..135694710,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10048942	0.92[ASN][1000 genomes]
rs10049233	0.92[ASN][1000 genomes]
rs10512981	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10935175	0.82[CEU][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs13082684	0.92[ASN][1000 genomes]
rs13097946	0.82[CEU][hapmap]
rs13322891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434196	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356664	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401545	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403766	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403767	1.00[ASN][1000 genomes]
rs1403770	0.85[CEU][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs1568349	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1568350	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843509	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17197552	0.82[CEU][hapmap]
rs2204259	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28449384	0.92[ASN][1000 genomes]
rs28570106	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576629	0.92[ASN][1000 genomes]
rs28855968	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875187	1.00[ASN][1000 genomes]
rs34522617	0.92[ASN][1000 genomes]
rs34767379	0.92[ASN][1000 genomes]
rs35722356	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36039354	0.92[ASN][1000 genomes]
rs4073308	0.85[CEU][hapmap]
rs4718	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55678980	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308637	1.00[ASN][1000 genomes]
rs56807950	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59063369	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66544356	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771997	0.82[CEU][hapmap]
rs6773469	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774289	0.82[CEU][hapmap]
rs6775778	0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs6779603	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786769	0.82[CEU][hapmap]
rs6802139	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807058	0.82[CEU][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs6807242	0.82[CEU][hapmap]
rs6807565	0.92[ASN][1000 genomes]
rs6809006	0.82[CEU][hapmap]
rs73222222	0.92[ASN][1000 genomes]
rs7427833	0.92[ASN][1000 genomes]
rs7433567	0.86[CEU][hapmap];0.92[ASN][1000 genomes]
rs7609938	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621331	0.82[CEU][hapmap]
rs7621396	0.82[CEU][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs7621425	0.82[CEU][hapmap]
rs7626676	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628848	0.92[ASN][1000 genomes]
rs7638129	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7640153	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7641070	0.92[ASN][1000 genomes]
rs7643661	0.82[CEU][hapmap]
rs870812	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908825	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289503	0.82[CEU][hapmap]
rs9808979	0.81[CEU][hapmap]
rs9812561	0.82[CEU][hapmap]
rs9813082	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814505	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814557	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[GIH][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9819440	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819988	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820189	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824558	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825239	0.82[CEU][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9826806	0.86[CEU][hapmap]
rs9829329	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9829476	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833699	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833799	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9834624	1.00[CEU][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836374	0.82[CEU][hapmap]
rs9836758	0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9837855	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839259	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9842864	0.92[ASN][1000 genomes]
rs9843725	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[GIH][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9844478	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846137	0.86[CEU][hapmap]
rs9848322	0.82[CEU][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9849088	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9853577	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs9854494	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862777	0.92[ASN][1000 genomes]
rs9864247	0.82[CEU][hapmap]
rs9864656	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864775	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868246	0.86[CEU][hapmap]
rs9870581	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872542	0.82[CEU][hapmap]
rs9875948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876837	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9883808	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9877722	MSL2	cis	cerebellum	SCAN
rs9877722	CRYBB2	trans	lymphoblastoid	seeQTL
rs9877722	RNF184	cis	multi-tissue	Pritchard
rs9877722	TMEM22	cis	cerebellum	SCAN
rs9877722	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135628200-135635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:135633600-135636400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:135635000-135636200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:135635200-135636000	Weak transcription	Psoas Muscle	Psoas
5	chr3:135635200-135636200	Enhancers	Liver	Liver
6	chr3:135635400-135635800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:135635400-135637200	Enhancers	Skeletal Muscle Male	skeletal muscle

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